1     M         0.955   0.959   0.994   1.146   1.148   1.189   1.001   1.006   1.051
2     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     N        -0.060  -0.093  -0.256  -0.130  -0.179  -0.448  -0.136  -0.186  -0.454
4     T        -2.310  -2.297  -2.093  -2.145  -2.114  -1.814  -1.842  -1.825  -1.571
5     T        -1.748  -1.754  -1.649  -1.595  -1.589  -1.450  -1.557  -1.561  -1.393
6     P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
7     I        -0.060  -0.118  -0.259  -0.102  -0.191  -0.428  -0.136  -0.224  -0.459
8     N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
9     I        -0.411  -0.405  -0.328  -0.713  -0.704  -0.568  -0.704  -0.695  -0.574
10    D        -1.748  -1.741  -1.648  -1.817  -1.806  -1.655  -1.557  -1.546  -1.392
11    K         0.955   0.959   0.994   0.953   0.955   1.014   1.001   1.006   1.051
12    W         0.955   0.959   0.994   1.183   1.186   1.223   1.001   1.006   1.051
13    L        -0.411  -0.394  -0.326  -0.720  -0.690  -0.568  -0.704  -0.675  -0.571
14    K        -0.060  -0.093  -0.256  -0.071  -0.121  -0.378  -0.136  -0.186  -0.454
15    E         0.955   0.959   0.994   0.907   0.911   0.972   1.001   1.006   1.051
16    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
17    E        -1.748  -1.720  -1.646  -1.593  -1.550  -1.466  -1.557  -1.526  -1.390
18    G        -0.973  -0.992  -1.063  -0.845  -0.876  -1.039  -0.989  -1.010  -1.074
19    L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
20    L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
21    K        -0.060  -0.024  -0.248  -0.001   0.050  -0.283  -0.136  -0.081  -0.440
22    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
23    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
24    V        -0.060  -0.118  -0.259  -0.112  -0.202  -0.432  -0.136  -0.224  -0.459
25    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
26    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
27    Y        -0.411  -0.381  -0.323  -0.435  -0.385  -0.301  -0.704  -0.654  -0.566
28    C         0.955   0.959   0.994   1.076   1.080   1.125   1.001   1.006   1.051
29    L        -1.185  -1.207  -1.095  -1.444  -1.476  -1.273  -1.273  -1.290  -1.114
30    H        -0.973  -0.961  -1.060  -0.741  -0.723  -0.885  -0.989  -0.974  -1.071
31    K        -1.185  -1.208  -1.095  -1.286  -1.324  -1.138  -1.273  -1.292  -1.114
32    G        -0.060  -0.118  -0.259  -0.097  -0.184  -0.418  -0.136  -0.224  -0.459
33    G        -0.060  -0.118  -0.259  -0.097  -0.184  -0.418  -0.136  -0.224  -0.459
34    F        -0.973  -0.885  -1.047  -0.745  -0.621  -0.852  -0.989  -0.874  -1.055
35    T         0.955   0.959   0.994   0.973   0.977   1.031   1.001   1.006   1.051
36    V        -0.060  -0.049  -0.253  -0.112  -0.097  -0.421  -0.136  -0.118  -0.448
37    M         0.955   0.959   0.994   1.146   1.148   1.189   1.001   1.006   1.051
38    I        -0.060  -0.024  -0.248  -0.105  -0.051  -0.413  -0.136  -0.081  -0.440
39    V         0.955   0.959   0.994   0.881   0.883   0.948   1.001   1.006   1.051
40    G         0.955   0.959   0.994   0.894   0.898   0.960   1.001   1.006   1.051
41    G         0.955   0.959   0.994   0.894   0.898   0.960   1.001   1.006   1.051
42    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
43    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
44    E        -0.411  -0.405  -0.328  -0.566  -0.560  -0.416  -0.704  -0.695  -0.574
45    R         0.955   0.959   0.994   1.031   1.035   1.085   1.001   1.006   1.051
46    T        -0.060  -0.049  -0.253   0.038   0.053  -0.237  -0.136  -0.118  -0.448
47    G        -0.060  -0.093  -0.256  -0.092  -0.136  -0.411  -0.136  -0.186  -0.454
48    Y         0.955   0.959   0.994   1.089   1.091   1.137   1.001   1.006   1.051
49    H         0.955   0.959   0.994   1.095   1.099   1.143   1.001   1.006   1.051
50    I         0.955   0.959   0.994   0.894   0.900   0.960   1.001   1.006   1.051
51    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
52    P        -0.060  -0.093  -0.256   0.061   0.024  -0.279  -0.136  -0.186  -0.454
53    T         0.955   0.959   0.994   0.973   0.977   1.031   1.001   1.006   1.051
54    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
55    E         0.955   0.959   0.994   0.907   0.911   0.972   1.001   1.006   1.051
56    W        -0.411  -0.394  -0.326  -0.342  -0.314  -0.225  -0.704  -0.675  -0.571
57    F         0.955   0.959   0.994   1.063   1.066   1.114   1.001   1.006   1.051
58    Y        -0.411  -0.372  -0.321  -0.418  -0.351  -0.280  -0.704  -0.638  -0.563
59    Q         0.955   0.959   0.994   1.050   1.069   1.102   1.001   1.006   1.051
60    K        -1.748  -1.752  -1.647  -1.671  -1.675  -1.503  -1.557  -1.558  -1.392
61    K         0.955   0.959   0.994   0.953   0.955   1.014   1.001   1.006   1.051
62    G         0.955   0.959   0.994   0.894   0.898   0.960   1.001   1.006   1.051
63    S        -2.310  -2.297  -2.093  -2.045  -2.020  -1.722  -1.842  -1.825  -1.571
64    M         0.955   0.959   0.994   1.146   1.148   1.189   1.001   1.006   1.051
65    L        -1.748  -1.754  -1.649  -1.585  -1.596  -1.446  -1.557  -1.561  -1.393
66    L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
67    K         0.955   0.959   0.994   0.953   0.955   1.014   1.001   1.006   1.051
68    V         0.955   0.959   0.994   0.881   0.883   0.948   1.001   1.006   1.051
69    V         0.955   0.959   0.994   0.881   0.883   0.948   1.001   1.006   1.051
70    D         0.955   0.959   0.994   0.901   0.912   0.966   1.001   1.006   1.051
71    E        -0.060  -0.093  -0.256  -0.089  -0.133  -0.405  -0.136  -0.186  -0.454
72    T        -0.060  -0.093  -0.256  -0.079  -0.128  -0.380  -0.136  -0.186  -0.454
73    D        -0.973  -1.045  -1.068  -1.030  -1.146  -1.196  -0.989  -1.078  -1.080
74    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    F         0.955   0.959   0.994   1.063   1.066   1.114   1.001   1.006   1.051
79    I        -0.973  -0.992  -1.063  -0.889  -0.922  -1.062  -0.989  -1.010  -1.074
80    D         0.955   0.959   0.994   0.901   0.912   0.966   1.001   1.006   1.051
81    I         0.955   0.959   0.994   0.894   0.900   0.960   1.001   1.006   1.051
82    I        -0.973  -0.905  -1.053  -0.959  -0.858  -1.062  -0.989  -0.900  -1.063
83    I         0.955   0.959   0.994   0.894   0.900   0.960   1.001   1.006   1.051
84    N        -0.973  -0.992  -1.064  -1.013  -1.036  -1.144  -0.989  -1.012  -1.076
85    E         0.955   0.959   0.994   0.907   0.911   0.972   1.001   1.006   1.051
86    G        -0.060  -0.024  -0.248  -0.097  -0.043  -0.398  -0.136  -0.081  -0.440
87    D        -0.060  -0.118  -0.259  -0.089  -0.171  -0.410  -0.136  -0.224  -0.459
88    S        -0.973  -0.961  -1.060  -0.735  -0.716  -0.900  -0.989  -0.974  -1.071
89    Y        -0.060  -0.093  -0.256   0.115   0.067  -0.190  -0.136  -0.186  -0.454
90    L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
91    L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
92    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
93    G        -1.185  -1.140  -1.092  -1.330  -1.275  -1.137  -1.273  -1.222  -1.110
94    N         0.955   0.959   0.994   0.874   0.884   0.942   1.001   1.006   1.051
95    V        -0.411  -0.415  -0.330  -0.663  -0.675  -0.517  -0.704  -0.712  -0.579
96    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
97    H         0.955   0.959   0.994   1.095   1.099   1.143   1.001   1.006   1.051
98    S        -0.060  -0.093  -0.256  -0.058  -0.099  -0.322  -0.136  -0.186  -0.454
99    P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
100   V        -0.060  -0.049  -0.253  -0.066  -0.052  -0.337  -0.136  -0.118  -0.448
101   R         0.955   0.959   0.994   1.031   1.035   1.085   1.001   1.006   1.051
102   F        -0.411  -0.430  -0.334  -0.435  -0.478  -0.323  -0.704  -0.739  -0.585
103   A        -0.060  -0.049  -0.253   0.109   0.124  -0.233  -0.136  -0.118  -0.448
104   D        -0.411  -0.394  -0.326  -0.703  -0.664  -0.555  -0.704  -0.675  -0.571
105   T         0.955   0.959   0.994   0.973   0.977   1.031   1.001   1.006   1.051
106   V        -0.411  -0.430  -0.334  -0.705  -0.749  -0.573  -0.704  -0.739  -0.585
107   G         0.955   0.959   0.994   0.894   0.898   0.960   1.001   1.006   1.051
108   I        -0.973  -0.885  -1.047  -1.051  -0.911  -1.181  -0.989  -0.874  -1.055
109   V         0.955   0.959   0.994   0.881   0.883   0.948   1.001   1.006   1.051
110   V        -0.060  -0.118  -0.259  -0.118  -0.210  -0.445  -0.136  -0.224  -0.459
111   E         0.955   0.959   0.994   0.907   0.911   0.972   1.001   1.006   1.051
112   Q         0.955   0.959   0.994   1.050   1.069   1.102   1.001   1.006   1.051
113   D        -0.060  -0.118  -0.259  -0.077  -0.158  -0.389  -0.136  -0.224  -0.459
114   R         0.955   0.959   0.994   1.031   1.035   1.085   1.001   1.006   1.051
115   P         0.955   0.959   0.994   0.914   0.918   0.978   1.001   1.006   1.051
116   G        -1.748  -1.707  -1.640  -1.585  -1.524  -1.437  -1.557  -1.512  -1.385
117   G        -0.973  -0.992  -1.064  -0.971  -1.005  -1.096  -0.989  -1.012  -1.076
118   E        -2.310  -2.297  -2.093  -2.136  -2.134  -1.805  -1.842  -1.825  -1.571
119   N        -1.748  -1.719  -1.645  -1.851  -1.804  -1.677  -1.557  -1.526  -1.390
120   D         0.955   0.959   0.994   0.901   0.912   0.966   1.001   1.006   1.051
121   K        -0.973  -0.961  -1.060  -0.873  -0.865  -0.987  -0.989  -0.974  -1.071
122   I        -1.748  -1.784  -1.649  -1.781  -1.830  -1.602  -1.557  -1.589  -1.393
123   R         0.955   0.959   0.994   1.031   1.035   1.085   1.001   1.006   1.051
124   W         0.955   0.959   0.994   1.183   1.186   1.223   1.001   1.006   1.051
125   Y         0.955   0.959   0.994   1.089   1.091   1.137   1.001   1.006   1.051
126   C         0.955   0.959   0.994   1.076   1.080   1.125   1.001   1.006   1.051
127   S        -1.748  -1.707  -1.640  -1.634  -1.549  -1.477  -1.557  -1.512  -1.385
128   H        -1.748  -1.741  -1.648  -1.767  -1.748  -1.587  -1.557  -1.546  -1.392
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   C         0.955   0.959   0.994   1.076   1.080   1.125   1.001   1.006   1.051
132   R        -1.185  -1.176  -1.095  -1.225  -1.209  -1.058  -1.273  -1.259  -1.114
133   Q        -0.973  -0.992  -1.063  -0.951  -0.974  -1.072  -0.989  -1.010  -1.074
134   V        -0.411  -0.414  -0.330  -0.705  -0.716  -0.564  -0.704  -0.711  -0.578
135   V        -0.973  -0.937  -1.057  -1.057  -1.000  -1.201  -0.989  -0.940  -1.067
136   H        -0.060   0.015  -0.245   0.140   0.243  -0.157  -0.136  -0.023  -0.436
137   E         0.955   0.959   0.994   0.907   0.911   0.972   1.001   1.006   1.051
138   S        -1.748  -1.720  -1.646  -1.603  -1.551  -1.468  -1.557  -1.526  -1.390
139   E        -1.185  -1.163  -1.095  -1.185  -1.155  -1.025  -1.273  -1.247  -1.114
140   L        -0.060  -0.093  -0.256   0.062   0.009  -0.289  -0.136  -0.186  -0.454
141   Q        -1.185  -1.176  -1.095  -1.102  -1.078  -0.947  -1.273  -1.259  -1.114
142   M        -1.185  -1.196  -1.096  -1.218  -1.221  -1.037  -1.273  -1.279  -1.115
143   L        -0.973  -0.941  -1.057  -0.975  -0.929  -1.140  -0.989  -0.948  -1.067
144   D         0.955   0.959   0.994   0.901   0.912   0.966   1.001   1.006   1.051
145   L         0.955   0.959   0.994   0.868   0.872   0.936   1.001   1.006   1.051
146   G         0.955   0.959   0.994   0.894   0.898   0.960   1.001   1.006   1.051
147   T         0.955   0.959   0.994   0.973   0.977   1.031   1.001   1.006   1.051
148   Q         0.955   0.959   0.994   1.050   1.069   1.102   1.001   1.006   1.051
149   V        -0.411  -0.408  -0.329  -0.705  -0.703  -0.563  -0.704  -0.700  -0.577
150   K         0.955   0.959   0.994   0.953   0.955   1.014   1.001   1.006   1.051
151   E        -0.973  -0.992  -1.064  -0.957  -0.981  -1.084  -0.989  -1.012  -1.076
152   A         0.955   0.959   0.994   1.101   1.104   1.149   1.001   1.006   1.051
153   I        -0.060  -0.118  -0.259  -0.102  -0.191  -0.428  -0.136  -0.224  -0.459
154   L        -0.973  -1.011  -1.063  -1.064  -1.128  -1.212  -0.989  -1.035  -1.075
155   D        -1.748  -1.752  -1.647  -1.754  -1.749  -1.580  -1.557  -1.558  -1.392
156   F        -0.060  -0.024  -0.248   0.115   0.164  -0.177  -0.136  -0.081  -0.440
157   E        -1.185  -1.208  -1.095  -1.384  -1.412  -1.210  -1.273  -1.292  -1.114
158   N        -1.185  -1.176  -1.094  -1.358  -1.343  -1.165  -1.273  -1.259  -1.114
159   D        -0.411  -0.415  -0.330  -0.703  -0.707  -0.564  -0.704  -0.712  -0.579
160   V        -1.748  -1.784  -1.649  -1.873  -1.938  -1.714  -1.557  -1.589  -1.393
161   E        -0.973  -1.011  -1.063  -0.973  -1.023  -1.106  -0.989  -1.035  -1.075
162   K        -1.185  -1.209  -1.096  -1.239  -1.281  -1.099  -1.273  -1.293  -1.115
163   R         0.955   0.959   0.994   1.031   1.035   1.085   1.001   1.006   1.051
164   T         0.955   0.959   0.994   0.973   0.977   1.031   1.001   1.006   1.051
165   C         0.955   0.959   0.994   1.076   1.080   1.125   1.001   1.006   1.051
166   F        -0.973  -0.972  -1.059  -0.853  -0.858  -0.957  -0.989  -0.986  -1.070
167   H        -1.748  -1.720  -1.646  -1.650  -1.611  -1.478  -1.557  -1.526  -1.390
168   C         0.955   0.959   0.994   1.076   1.080   1.125   1.001   1.006   1.051
169   K        -0.060  -0.093  -0.256  -0.084  -0.134  -0.389  -0.136  -0.186  -0.454
170   T        -0.060  -0.118  -0.259  -0.024  -0.115  -0.363  -0.136  -0.224  -0.459
171   L        -0.411  -0.381  -0.323  -0.728  -0.675  -0.570  -0.704  -0.654  -0.566
172   N        -0.411  -0.405  -0.328  -0.594  -0.583  -0.439  -0.704  -0.695  -0.574
173   Y        -1.748  -1.732  -1.645  -1.567  -1.549  -1.423  -1.557  -1.539  -1.389
174   A        -0.973  -1.045  -1.068  -0.663  -0.770  -0.808  -0.989  -1.078  -1.080
175   R        -0.973  -0.992  -1.064  -0.815  -0.843  -0.958  -0.989  -1.012  -1.076
176   P        -0.060  -0.049  -0.253  -0.045  -0.029  -0.331  -0.136  -0.118  -0.448
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   N        -1.155  -1.151  -1.091  -1.216  -1.210  -1.143  -1.220  -1.213  -1.108
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/P47096
Output conservation file - output/P47096
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
